Phylogenetics and Evolutionary Dynamics of ()

Hannah McPherson BSc (Hons) University of New South Wales

A thesis submitted for the degree of Doctor of Philosophy University of New England

September 2008

Acknowledgments

Many thanks to my three supervisors, Darren Crayn, Caroline Gross and Maurizio Rossetto. I could not have wished to work with three more enthusiastic and positive people. I have learnt so much from you and it has been really inspiring and lots of fun.

I gratefully acknowledge the University of New England, the Australian Biological Resources Study and the Australian Postgraduate Award for funding my studies. Also the Australian Systematic Society for awarding me the Hansjörg Eichler Scientific Research Fund for fieldwork in South , and the Friends’ of the Royal Botanic Gardens and the University of New England for funding to attend the 10th Evolutionary Biology meeting in Marseilles in 2006.

Many thanks also to Professor Robert Henry and Associate Professor Jeremy Bruhl for reviewing draft chapters for my upgrade from MSc to PhD.

My colleagues at the Royal Botanic Gardens in Sydney have been wonderfully supportive both professionally and personally. In particular I would like to thank Tim Entwisle, Brett Summerell, Karen Wilson and Louisa Murray who have been extremely encouraging throughout the course of my project. It has been a pleasure to be a part of the Molecular Laboratory team at the Gardens. Thanks especially to Carolyn Porter and Margaret Heslewood for patiently teaching me so much. To the other lab folk – big thanks – Paul Rymer, Karen Sommerville, Mike Whitehead, Rohan Mellick, Yola Metti, Andrew Perkins, John Thomson, and Nick Yee.

The following herbaria generously supplied herbarium data: BRI, NE, NSW, MEL, HO, AD, PERTH for which I am very grateful. Thanks also to Joy Thompson, Ryonen Butcher, Trisha Downing, Andrew Perkins, Maurizio Rossetto, Penny Butcher, Darren Crayn, Caroline Gross and Natalie Papworth for providing expertise, specimens, or DNA used in the present study.

Thank you to my many field work assistants: Anton Perkins, Gill Towler, Kathi Downs, Louisa Murray, Linn Linn Lee, Darryl McPherson, Darren Crayn, Margaret Heslewood, Elizabeth Brown, Peter Wilson, Bob Coveny, Chris Quinn, Stephen Skinner, Richard Greenhill, Rachel Gallagher, Phil Pisanu and Jenny Mason.

Margaret Heslewood, Anton Perkins, Sarah Bunn, Lucy Nairn, Chris Allen, Gary Chapple, Linn Linn Lee, Gill Towler, Sally Waller, were wonders proof-reading and helping me solve problems with data, images and mapping.

Thanks are also due to Pierre Taberlet at the Université Joseph Fournier, Grenoble; staff at the Jodrell Laboratory, Kew, London; the Science Department, Oxford; Chris Humphries and Pat Wolesley, Botany Department at the Natural History Museum, London; Peter Weston, Royal Botanic Gardens, Sydney for valuable feedback on presentations.

Thanks to my family Sarah Bunn and Anna Bunn Decombes, Fiona Bunn, Darryl McPherson, Jesse McPherson and Heather McPherson; ladies who brunch and Julie Taylor for spurring me on and also taking me away from it sometimes.

To Anton Perkins - Field Assistant (First Class) - a well deserved promotion - thanks for everything. Abstract

Tetratheca Sm. (Elaeocarpaceae) is an endemic Australian of small shrubs distributed mainly across the southern part of the continent. Most species are narrowly endemic or highly disjunct: very few are widespread. Adequate conservation planning relies on comprehensive knowledge of the evolutionary history of the taxa, strength and direction of current gene flow and connectivity between populations, and the occurrence of local adaptation or drift.

In this study I investigated species distribution patterns and processes driving speciation in the Australian endemic genus Tetratheca at a variety of taxonomic, geographic and temporal scales. Evolutionary processes were explored using a hierarchy of molecular approaches: phylogenetic reconstruction, comparative phylogeography and population genetics.

Phylogenetic analyses of plastid and nuclear DNA sequence data for over 85% of the known species confirmed that Tetratheca is monophyletic, with several lineages in and only two in the eastern states of the continent. Resolution within some lineages was poor and there were minor points of conflict between phylogenies, implying a role for incomplete lineage sorting (ILS) or hybridisation in the evolution of the genus.

Phylogeographic and population genetic analyses using data from a range of chloroplast and novel nuclear microsatellite loci was undertaken on the and T. ciliata-T.stenocarpa species complexes. The results helped to clarify phylogenetic ambiguities, and support the hypothesis that ILS is more influential than hybridisation in explaining phylogenetic incongruence in the studied taxa.

The present study shows that in the case of Tetratheca, a recently derived and rapidly evolving component of the Australian flora, patterns of genetic diversity at the micro- evolutionary scale can help with interpretation of macroevolutionary processes in the genus. It thereby confirms that comparative studies of a range of species, applied at a variety of hierarchical scales, can be particularly useful for understanding evolutionary processes and genetic diversity of any single species.

Table of contents

Chapter 1 Introduction ...... 1 1.1 Chapter overview...... 2 1.2 Background to the Australian flora ...... 2 1.3 Elaeocarpaceae ...... 3 1.4 Tetratheca and allies...... 4 1.5 Biogeography and endemism in Tetratheca...... 7 1.6 Approaches and molecular tools...... 8 1.6.1 Phylogeny ...... 8 1.6.2 Phylogeography...... 9 1.6.3 Population genetics...... 11 1.6.4 A hierarchical approach for exploring genetic diversity and distribution patterns…………………………………………………………………….12 1.7 Project aims ...... 13 Chapter 2 Molecular phylogenetics of Tetratheca (Elaeocarpaceae) ...... 14 2.1 Introduction ...... 14 2.2 Materials and Methods ...... 17 2.2.1 Taxa and plant material ...... 17 2.2.2 Nuclear and chloroplast data ...... 18 2.2.3 DNA isolation...... 26 2.2.4 Amplification using Polymerase Chain Reaction (PCR) ...... 26 2.2.5 Sequencing and alignment...... 27 2.2.6 Phylogenetic analyses...... 29 2.3 Results ...... 33 2.3.1 Nuclear ITS data...... 33 2.3.2 Chloroplast trnL-trnF data ...... 39 2.3.3 Combined analysis of ITS and trnL-trnF ...... 42 2.4 Discussion...... 46 2.4.1 Monophyly of Tetratheca...... 47 2.4.2 Western origin for Tetratheca and differentiation of an eastern clade...... 48 2.4.3 Affinities of the Kangaroo Island taxa ...... 49 2.4.4 Testing morphological groups with molecular data ...... 50 2.4.5 Evidence of incomplete lineage sorting or hybridisation in the evolutionary history of Tetratheca ...... 56 2.5 Conclusions ...... 57 Chapter 3 Comparative phylogeography of two species complexes within Tetratheca.. ……………………………………………………………………………..59 3.1 Introduction ...... 59 3.1.1 Chloroplast microsatellites ...... 60 3.2 Materials and Methods ...... 62 3.2.1 Sampling...... 62 3.2.2 Plant material and DNA isolation...... 63 3.2.3 Chloroplast microsatellites ...... 63 3.2.4 Locus screening I: amplification using PCR ...... 66 3.2.5 Locus screening II: multiplexing PCR reactions...... 67 3.2.6 Chloroplast microsatellite analysis...... 68 3.2.7 Data analysis...... 68 3.3 Tetratheca pilosa group...... 72 3.3.1 Introduction ...... 72 3.3.2 Sampling...... 76 3.3.3 Chloroplast microsatellite analysis...... 76 3.3.4 Results ...... 76 3.3.5 Discussion...... 93 3.4 and T. stenocarpa...... 97 3.4.1 Introduction ...... 97 3.4.2 Sampling...... 99 3.4.3 Chloroplast microsatellite analysis...... 99 3.4.4 Results ...... 100 3.4.5 Discussion...... 113 3.5 General conclusions...... 115 Chapter 4 Population genetic diversity and structure within and among populations of Tetratheca ciliata and T. stenocarpa...... 118 4.1 Introduction ...... 118 4.2 Materials and Methods ...... 120 4.2.1 Development and characterisation of a nuclear SSR library for Tetratheca 120 4.2.2 Sampling...... 124 4.2.3 Plant material and DNA isolation...... 124 4.2.4 Locus selection...... 126 4.2.5 Locus screening I: amplification using PCR ...... 127 4.2.6 Locus screening II: multiplexing PCR reactions...... 128 4.2.7 Nuclear microsatellite analysis...... 128 4.2.8 Error checking...... 129 4.2.9 Data analysis...... 130 4.3 Results ...... 133 4.3.1 A nuclear SSR library for Tetratheca...... 133 4.3.2 Locus screening and error checking ...... 133 4.3.3 Diversity statistics...... 134 4.3.4 Hardy-Weinberg and genotypic linkage equilibria ...... 135 4.3.5 Bottlenecks ...... 136 4.3.6 Population differentiation...... 137 4.4 Discussion...... 144 4.4.1 Species boundaries and hybridisation...... 145 4.4.2 Geographic structure of genetic variation ...... 146 Chapter 5 Discussion and conclusions...... 151 Summary...... 151 Conclusions ...... 157 References ...... 159